From fddacbf462e3dfb7f91a3655eca33b90aae2da2d Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 8 Feb 2024 10:39:40 -0500
Subject: [PATCH 1/2] patch the environment file to pin Julia to 1.9.5 + git
 syntax fix

git syntax fixes - quotes around sign in, default upstream is origin

modify mac sed command because apparently the syntax is different thanks stackoverflow https://stackoverflow.com/a/19457213

switch julia to 1.9.1 in CI
---
 .github/workflows/CI.yml   | 4 ++++
 .github/workflows/docs.yml | 8 +++++---
 2 files changed, 9 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index c02c67a985..43a9d7ad60 100644
--- a/.github/workflows/CI.yml
+++ b/.github/workflows/CI.yml
@@ -62,6 +62,8 @@ jobs:
         uses: actions/checkout@v3
 
       # configures the mamba environment manager and builds the environment
+      - name: Patch Environment File
+        run: sed -i '' 's/  - conda-forge::julia>=1.8.5,!=1.9.0/  - conda-forge::julia=1.9.1/' environment.yml
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -112,6 +114,8 @@ jobs:
         uses: actions/checkout@v3
 
       # configures the mamba environment manager and builds the environment
+      - name: Patch Environment File
+        run: sed -i 's/  - conda-forge::julia>=1.8.5,!=1.9.0/  - conda-forge::julia=1.9.1/' environment.yml
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2
         with:
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
index 046b22fcdb..d3c9de06eb 100644
--- a/.github/workflows/docs.yml
+++ b/.github/workflows/docs.yml
@@ -16,6 +16,8 @@ jobs:
         shell: bash -l {0}
     steps:
       - uses: actions/checkout@v2
+      - name: Patch Environment File
+        run: sed -i 's/  - conda-forge::julia>=1.8.5,!=1.9.0/  - conda-forge::julia=1.9.1/' environment.yml
       - name: Setup Mambaforge Python 3.7
         uses: conda-incubator/setup-miniconda@v2
         with:
@@ -59,8 +61,8 @@ jobs:
       - name: Make documentation - to publish
         if: ${{  github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
         run: |
-          git config user.name github-actions
-          git config user.email github-actions@github.com
+          git config user.name "github-actions"
+          git config user.email "github-actions@github.com"
           cd documentation
           make html
       - name: Check documentation links
@@ -72,4 +74,4 @@ jobs:
         if: ${{  github.event_name == 'push' && github.repository == 'ReactionMechanismGenerator/RMG-Py' }}
         run: |
           touch build/html/.nojekyll
-          cd build/html; git add -A .; git commit -m "Automated documentation rebuild"; git push official gh-pages
+          cd build/html; git add -A .; git commit -m "Automated documentation rebuild"; git push origin gh-pages

From 51924d98ed65bac069cbbde0ab7c894979c567a5 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Thu, 8 Feb 2024 10:57:37 -0500
Subject: [PATCH 2/2] update Docker image with stable Julia version

 - patch the environment file when building Docker image to a version that @calvinp0 manually tested to work on windows
 - set an env variable before building RMS to fix an issue with precompilation

Thanks Calvin!
---
 Dockerfile | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/Dockerfile b/Dockerfile
index 803374c02a..a5c38c33b1 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -42,8 +42,10 @@ WORKDIR /rmg
 RUN git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-Py.git && \
     git clone --single-branch --branch main --depth 1 https://github.com/ReactionMechanismGenerator/RMG-database.git
 
-# build the conda environment
 WORKDIR /rmg/RMG-Py
+# patch the env file to a specific version of Julia that we know to be working on all platforms
+RUN sed -i 's/  - conda-forge::julia>=1.8.5,!=1.9.0/  - conda-forge::julia=1.9.4/' environment.yml
+# build the conda environment
 RUN conda env create --file environment.yml && \
     conda clean --all --yes
 
@@ -61,6 +63,8 @@ ENV PATH="$RUNNER_CWD/RMG-Py:$PATH"
 
 # 1. Build RMG
 # 2. Install and link Julia dependencies for RMS
+# setting this env variable fixes an issue with Julia precompilation on Windows
+ENV JULIA_CPU_TARGET="x86-64,haswell,skylake,broadwell,znver1,znver2,znver3,cascadelake,icelake-client,cooperlake,generic"
 RUN make && \
     julia -e 'using Pkg; Pkg.add(PackageSpec(name="PyCall",rev="master")); Pkg.add(PackageSpec(name="ReactionMechanismSimulator",rev="main")); using ReactionMechanismSimulator' && \
     python -c "import julia; julia.install(); import diffeqpy; diffeqpy.install()"